CSAG3

Summary

CSAG3 (CSAG family member 3, HGNC:26237) is a protein-coding gene on chromosome Xq28, encoding Chondrosarcoma-associated gene 2/3 protein (Q9Y5P2). Drug-resistance related protein, its expression is associated with the chemotherapy resistant and neoplastic phenotype.

Predicted to be involved in response to xenobiotic stimulus.

Source: NCBI Gene 389903 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001129826

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26237
Approved symbol	CSAG3
Name	CSAG family member 3
Location	Xq28
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000268916
Ensembl biotype	protein_coding
OMIM	301097
Entrez	389903

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000599845, ENST00000617158, ENST00000638835, ENST00000921341

RefSeq mRNA: 2 — MANE Select: NM_001129826 NM_001129826, NM_001129828

Canonical transcript exons

ENST00000599845 — 2 exons

Exon	Start	End
ENSE00003806425	152759218	152759684
ENSE00003807311	152759843	152760219

Expression profiles

Bgee: expression breadth broad, 75 present calls, max score 83.12.

Top tissues by expression

259 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.12	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	74.40	gold quality
triceps brachii	UBERON:0001509	74.10	gold quality
gluteal muscle	UBERON:0002000	74.09	gold quality
parotid gland	UBERON:0001831	71.54	gold quality
left testis	UBERON:0004533	67.84	gold quality
right testis	UBERON:0004534	66.65	gold quality
testis	UBERON:0000473	65.95	gold quality
biceps brachii	UBERON:0001507	63.18	gold quality
spleen	UBERON:0002106	60.80	gold quality
hair follicle	UBERON:0002073	60.79	gold quality
heart right ventricle	UBERON:0002080	60.49	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	59.60	gold quality
decidua	UBERON:0002450	59.21	gold quality
lymph node	UBERON:0000029	59.13	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	57.69	gold quality
inferior olivary complex	UBERON:0002127	57.59	gold quality
deltoid	UBERON:0001476	56.39	gold quality
buccal mucosa cell	CL:0002336	56.27	gold quality
quadriceps femoris	UBERON:0001377	56.17	gold quality
mammary duct	UBERON:0001765	56.11	gold quality
vastus lateralis	UBERON:0001379	55.91	gold quality
epithelium of mammary gland	UBERON:0003244	55.72	gold quality
myocardium	UBERON:0002349	55.20	gold quality
esophagus squamous epithelium	UBERON:0006920	55.12	gold quality
epithelium of esophagus	UBERON:0001976	54.96	gold quality
endothelial cell	CL:0000115	54.80	gold quality
nasal cavity epithelium	UBERON:0005384	54.73	gold quality
cartilage tissue	UBERON:0002418	54.24	gold quality
trabecular bone tissue	UBERON:0002483	54.10	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	395.79
E-ANND-3	no	0.81

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (2): CSAG1 (ENSG00000198930), CSAG2 (ENSG00000268902)

Protein

Protein identifiers

Chondrosarcoma-associated gene 2/3 protein — Q9Y5P2 (reviewed: Q9Y5P2)

Alternative names: Cancer/testis antigen 24.2, Taxol-resistant-associated gene 3 protein

All UniProt accessions (1): Q9Y5P2

UniProt curated annotations — full annotation on UniProt →

Function. Drug-resistance related protein, its expression is associated with the chemotherapy resistant and neoplastic phenotype. May also be linked to the malignant phenotype.

Tissue specificity. Weakly expressed in kidney. Expressed in various tumor cell lines including carcinomas, myeloid and lymphoid malignancies, melanomas and prostate cancer. Overexpressed in taxol-resistant breast cancer line MDA 435TR and the doxorubicin-resistant multiple myelanoma lines RPMI-8226/Dox40 and RPMI-8226/MDR10V.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9Y5P2-1	1, Long, TRAG-3L	yes
Q9Y5P2-2	2, Short, TRAG-3S
Q9Y5P2-3	3

RefSeq proteins (2): NP_001123298, NP_001123300 (=MANE)

Domains & families (InterPro)

UniProt features (10 total): sequence conflict 5, splice variant 3, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y5P2-F1	56.41	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 16 (showing top): RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP, chrXq28, MIR3942_3P, MIR6819_5P, MIR6737_5P, MIR6812_5P, MIR6747_5P, WANG_SMARCE1_TARGETS_DN, JAEGER_METASTASIS_UP, RICKMAN_HEAD_AND_NECK_CANCER_B

GO Biological Process (1): response to xenobiotic stimulus (GO:0009410)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to chemical	1
binding	1

Protein interactions and networks

STRING

410 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSAG3	MAGEA3	P43357	721
CSAG3	MAGEA2B	P43356	670
CSAG3	MAGEA10	P43363	657
CSAG3	CTAG2	O75638	575
CSAG3	MAGEA12	P43365	570
CSAG3	CTAG1A	P78358	542
CSAG3	CT47A11	Q5JQC4	507
CSAG3	CT45A1	Q5HYN5	506
CSAG3	SPANXA1	Q9NS26	505
CSAG3	GAGE2A	Q6NT46	480
CSAG3	CT55	Q8WUE5	479
CSAG3	PASD1	Q8IV76	473
CSAG3	PRAME	P78395	448
CSAG3	MAGEB6	Q8N7X4	447
CSAG3	SSX4	O60224	446

IntAct

8 interactions, top by confidence:

A	B	Type	Score
SIRT1	CSAG2	psi-mi:“MI:0915”(physical association)	0.640
CSAG2	SIRT1	psi-mi:“MI:0915”(physical association)	0.640
CSAG2	SIRT1	psi-mi:“MI:0403”(colocalization)	0.640
CSAG2	TP53	psi-mi:“MI:0197”(deacetylation reaction)	0.440
CSAG2	CAMK2D	psi-mi:“MI:0914”(association)	0.350

BioGRID (1): CSAG3 (Biochemical Activity)

ESM2 similar proteins: A0A1B0GVR7, A0A6G7KUU3, A0PJW8, B1AK76, B8UU74, D3ZF18, O12159, O15926, O46660, O95567, P03424, P05900, P05901, P05913, P0C8P5, P0DPG3, P12452, P19718, P20877, P20920, P26035, P28970, P32544, P33482, P35977, P92524, Q02781, Q1X6Y8, Q1X6Y9, Q2M2E5, Q2YDM5, Q32M92, Q5K130, Q5TBE3, Q5VTH2, Q66104, Q6S6S5, Q6ZSB3, Q77MS7, Q8AII0

Diamond homologs: Q6PB30, Q9Y5P2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
CSAG2	“up-regulates activity”	SIRT1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

1 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	1
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

822 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:152759476:T:C	F36L	0.966
X:152759478:T:A	F36L	0.966
X:152759478:T:G	F36L	0.966
X:152759374:T:A	W2R	0.920
X:152759374:T:C	W2R	0.920
X:152759844:T:C	F106L	0.907
X:152759846:C:A	F106L	0.907
X:152759846:C:G	F106L	0.907
X:152759440:T:C	F24L	0.906
X:152759442:C:A	F24L	0.906
X:152759442:C:G	F24L	0.906
X:152759497:T:C	F43L	0.898
X:152759499:C:A	F43L	0.898
X:152759499:C:G	F43L	0.898
X:152759477:T:C	F36S	0.893
X:152759425:T:C	F19L	0.872
X:152759427:C:A	F19L	0.872
X:152759427:C:G	F19L	0.872
X:152759380:G:C	G4R	0.864
X:152759477:T:G	F36C	0.860
X:152759485:T:C	C39R	0.840
X:152759376:G:C	W2C	0.839
X:152759376:G:T	W2C	0.839
X:152759487:C:G	C39W	0.829
X:152759384:T:A	L5H	0.806
X:152759384:T:C	L5P	0.802
X:152759396:T:A	V9D	0.798
X:152759490:G:C	W40C	0.795
X:152759490:G:T	W40C	0.795
X:152759441:T:C	F24S	0.786

dbSNP variants (sampled 300 via entrez): RS113506057 (X:152708044 A>C), RS1156377608 (X:152759895 AC>A), RS1156556886 (X:152759100 G>C), RS1156728302 (X:152708807 G>A), RS1156870224 (X:152707963 G>C), RS1158065707 (X:152760326 C>G), RS1158360324 (X:152755653 T>G), RS1158405268 (X:152708291 T>C), RS1158548327 (X:152759561 G>A), RS1158963610 (X:152708354 G>A), RS1160188614 (X:152708051 T>C,G), RS1160654544 (X:152759984 C>G,T), RS1160768902 (X:152759151 A>G,T), RS1160973910 (X:152757627 A>G,T), RS1161008099 (X:152708215 C>A,G)

Disease associations

OMIM: gene MIM:301097 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
2-palmitoylglycerol	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Atrazine	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Okadaic Acid	decreases expression	1
Particulate Matter	increases abundance, increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.